Coloured stochastic multilevel multiset rewriting

From the phosphorylation state of a molecule to the volume of a cell, parameters are ubiquitous in systems biology. At the same time, most models involve static or dynamic compartments, for example to separate cells from their environment. We introduce coloured stochastic multilevel multiset rewriting, an expressive formalism for modelling systems with parameters and complex dynamic, multilevel compartment structures, and an extension of both multilevel multiset rewriting and coloured Petri nets. While being very expressive, it allows the direct and natural expression of biological ideas. We give some illustrative examples, demonstrating the use of parameters to handle cell states, position and volume, and variable rates. We further demonstrate the use of rules with complex right-hand sides for reproduction. We regard these examples as paving the way for more biologically relevant models. Categories and Subject Descriptors J.3 [Life and Medical Sciences]: Biology and genetics; D.3.2 [...

• Type: Journal
• Year: 2011
• Where: CMSB
• Authors: Nicolas Oury, Gordon D. Plotkin
• Keywords: Applied Computing, Cell Parameters, CMSB 2011, Coloured Petri Nets, Expressive Formalism